X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fext%2Fpymol%2FPymolCommands.java;h=08521a28aab9255f373b6788de26b6279739dd81;hb=c1e71094304dcd2b975c485416ec5e25cca30815;hp=ae91aa581954bec873a4314a28ad3fbfaf0b619e;hpb=0b6e9403e96ee9f0d41211b2f90130ff850c4e98;p=jalview.git
diff --git a/src/jalview/ext/pymol/PymolCommands.java b/src/jalview/ext/pymol/PymolCommands.java
index ae91aa5..08521a2 100644
--- a/src/jalview/ext/pymol/PymolCommands.java
+++ b/src/jalview/ext/pymol/PymolCommands.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ext.pymol;
import java.awt.Color;
@@ -106,21 +126,27 @@ public class PymolCommands extends StructureCommandsBase
@Override
public List superposeStructures(AtomSpecModel refAtoms,
- AtomSpecModel atomSpec, boolean isNucleotide)
+ AtomSpecModel atomSpec, AtomSpecType specType)
{
+
// https://pymolwiki.org/index.php/Super
List commands = new ArrayList<>();
- String refAtomsAlphaOnly = "("+getAtomSpec(refAtoms, true)+" and (altloc '' or altloc 'a'))";
- String atomSpec2AlphaOnly = "("+getAtomSpec(atomSpec, true)+" and (altloc '' or altloc 'a'))";
+ String refAtomsAlphaOnly = "(" + getAtomSpec(refAtoms, specType)
+ + " and (altloc '' or altloc 'a'))";
+ String atomSpec2AlphaOnly = "(" + getAtomSpec(atomSpec, specType)
+ + " and (altloc '' or altloc 'a'))";
// pair_fit mobile -> reference
- commands.add(new StructureCommand("pair_fit",
- atomSpec2AlphaOnly, refAtomsAlphaOnly));
+ // crashes when undo is enabled on 2.5.2 (incentive)
+ commands.add(new StructureCommand("undo_disable"));
+ commands.add(new StructureCommand("pair_fit", atomSpec2AlphaOnly,
+ refAtomsAlphaOnly));
+ commands.add(new StructureCommand("undo_enable"));
/*
* and show superposed residues as cartoon
*/
- String refAtomsAll = getAtomSpec(refAtoms, false);
- String atomSpec2All = getAtomSpec(atomSpec, false);
+ String refAtomsAll = getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY);
+ String atomSpec2All = getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY);
commands.add(new StructureCommand("show", "cartoon",
refAtomsAll + " " + atomSpec2All));
@@ -154,7 +180,7 @@ public class PymolCommands extends StructureCommandsBase
* @see https://pymolwiki.org/index.php/Selection_Macros
*/
@Override
- public String getAtomSpec(AtomSpecModel model, boolean alphaOnly)
+ public String getAtomSpec(AtomSpecModel model, AtomSpecType specType)
{
StringBuilder sb = new StringBuilder(64);
boolean first = true;
@@ -185,10 +211,14 @@ public class PymolCommands extends StructureCommandsBase
}
}
sb.append("/");
- if (alphaOnly)
+ if (specType == AtomSpecType.ALPHA)
{
sb.append("CA");
}
+ if (specType == AtomSpecType.PHOSPHATE)
+ {
+ sb.append("P");
+ }
}
}
return sb.toString();
@@ -262,7 +292,7 @@ public class PymolCommands extends StructureCommandsBase
StringBuilder sb = new StringBuilder(128);
sb.append("p.").append(attributeName).append("='")
.append(attributeValue).append("'");
- String atomSpec = getAtomSpec(atomSpecModel, false);
+ String atomSpec = getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY);
return new StructureCommand("iterate", atomSpec, sb.toString());
}
@@ -333,4 +363,11 @@ public class PymolCommands extends StructureCommandsBase
return CLOSE_PYMOL;
}
+ @Override
+ public List centerViewOn(List residues)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
}